Manganese in PDB 5ivj: Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid]

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid], PDB code: 5ivj was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.98 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.556, 62.516, 46.772, 90.00, 92.32, 90.00
R / Rfree (%)	15.9 / 18.9

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid] also contains other interesting chemical elements:

Fluorine

(F)

5 atoms

The binding sites of Manganese atom in the Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid] (pdb code 5ivj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid], PDB code: 5ivj:

Manganese binding site 1 out of 1 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid]


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4- Difluoropiperidin-1-Yl)Ethyl]-5-Fluoro-1H-Indazol-3-Yl}Amino) Pyridine-4-Carboxylic Acid] within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:12.1 occ:1.00 OE2 A:GLU485 2.1 14.6 1.0 O A:HOH741 2.2 16.1 1.0 O A:HOH732 2.2 14.2 1.0 NE2 A:HIS483 2.3 10.1 1.0 N07 A:6ED601 2.3 11.2 1.0 NE2 A:HIS571 2.3 13.3 1.0 CD A:GLU485 3.2 14.2 1.0 CE1 A:HIS571 3.2 12.0 1.0 C06 A:6ED601 3.2 9.9 1.0 CE1 A:HIS483 3.2 10.9 1.0 C08 A:6ED601 3.2 10.4 1.0 CD2 A:HIS483 3.3 8.6 1.0 CD2 A:HIS571 3.3 10.3 1.0 OE1 A:GLU485 3.5 18.9 1.0 O A:HOH848 4.2 31.9 1.0 ND1 A:HIS483 4.3 9.9 1.0 ND1 A:HIS571 4.3 8.7 1.0 CG A:HIS483 4.4 9.1 1.0 CG A:HIS571 4.4 8.1 1.0 O A:HOH728 4.5 34.0 1.0 OG A:SER491 4.5 15.4 1.0 CG A:GLU485 4.5 10.5 1.0 C05 A:6ED601 4.5 10.4 1.0 C09 A:6ED601 4.5 11.4 1.0

J.R.Horton, X.Liu, M.Gale, L.Wu, J.R.Shanks, X.Zhang, P.J.Webber, J.S.Bell, S.C.Kales, B.T.Mott, G.Rai, D.J.Jansen, M.J.Henderson, D.J.Urban, M.D.Hall, A.Simeonov, D.J.Maloney, M.A.Johns, H.Fu, A.Jadhav, P.M.Vertino, Q.Yan, X.Cheng. Structural Basis For KDM5A Histone Lysine Demethylase Inhibition By Diverse Compounds. Cell Chem Biol V. 23 769 2016.
ISSN: ESSN 2451-9456
PubMed: 27427228
DOI: 10.1016/J.CHEMBIOL.2016.06.006